Temporal changes in the genetic capacity of the Port Phillip Bay sediment microbiome to remove nitrogen

The external nitrogen load in Port Phillip Bay is estimated between 6000 and 9000 t N year-1. In the mid-1990s the Port Phillip Bay Environmental study identified that the majority of nitrogen compounds entering the bay are... [ view full abstract ]

The external nitrogen load in Port Phillip Bay is estimated between 6000 and 9000 t N year-1. In the mid-1990s the Port Phillip Bay Environmental study identified that the majority of nitrogen compounds entering the bay are removed by the sediment microbiome through the process of denitrification. The study identified that if microbial denitrification was compromised excessive nutrient loading could lead to eutrophic conditions. Within the sediment microbiome nitrogen compounds are transformed by enzymes transcribed from conserved functional genes. This study measured the temporal variation in the relative abundance of functional genes involved in nitrification (ammonia monooxygenase), denitrification (nitrate and nitrite reductase), anaerobic ammonium oxidation (16S rRNA specific for Anammox Bacteria) and nitrogen fixation (nitrogenase) at three sites in Port Phillip Bay (Centre of the Bay, Hobsons Bay and Long Reef). Changes in the relative abundance of functional genes was compared to changes in the environment. Environmental parameters (temperature, salinity, dissolved oxygen, chlorophyll-α fluorescence) were collected in situ from the overlying water column. Functional gene markers for denitrification were dominated at all three sites by cytochrome cd1- containing nitrite reductase (nirS) and not the copper-containing nitrite reductase (nirK). No seasonal change was identified in the abundance of nirS/K at Hobsons Bay or in the centre of the Bay. However, an increase in nirS was identified at Long Reef between January and December. The relative abundance of both archaeal ammonia oxidisers (AOA) and bacterial ammonia oxidisers (AOB) at the sediment water interface were negatively correlated with water temperature in Hobsons Bay and in the centre of the Bay. For example, the highest relative abundance of AOA was observed in August coinciding with the lowest water temperatures. This study identified that the proportion of the sediment microbiome involved in nitrification (converts ammonium to nitrate/nitrite), but not denitrification (converts nitrate/nitrite to gas), changes seasonally at two sites in Port Phillip Bay. Microbiomes respond to changes in their environment. Identifying the environmental drivers influencing nitrogen transformations within Port Phillip Bay will inform future management and monitoring programs.